Season 3

Complete listed story — includes the ending

1. The Weight of This Combination

While Cosima's condition is improving, Delphine takes over Rachel's duties at Dyad, but the two break up. Delphine shows Sarah a video of two Castor clones, Rudy and Seth, attempting to abduct Krystal Goderitch, a Leda clone; Rudy is the imprisoned clone in Marion's house. After Rudy tells Sarah to "count your sisters", she learns Helena is missing and further resents Mrs. S for taking part in her disappearance even though she did so to help free Sarah and Kira from Dyad. Later Topside official Ferdinand arrives to talk to Rachel. Sarah impersonates her to avoid him knowing of her condition. Sarah learns that Ferdinand took part in "Helsinki", assassinating six self aware Leda clones in Finland, and he is under Rachel's orders to kill those in the Clone Club, starting with Alison. Delphine manages to learn about Ferdinand's purpose through torturing the now brain-damaged Rachel and manages to have him call off the assassinations. Meanwhile, Alison decides to run for school trustee against Marci Coates to oppose Marci's plans on rezoning the school district. Seth breaks Rudy free.

2. Transitory Sacrifices of Crisis

Sarah learns from Art that Rudy and Seth assaulted a woman in a hotel and took a lock of her hair. Seth is revealed to be suffering from a degenerative disorder. Helena is being held in a controlled military zone and subjected to testing where her captor Doctor Virginia Coady learns of her pregnancy. Rudy and Seth search for the original clone tissue in Felix's apartment. Rudy holds Kira hostage to gather information from Sarah; he does not believe Sarah's claims that Ethan Duncan did not leave original tissue samples with her. When Seth suffers a seizure outside while holding a knife to Cal, Rudy retreats and ends Seth's suffering by killing him. Realizing Kira is not safe with Sarah, Cal moves with Kira to Iceland while Sarah goes to look for Helena. Meanwhile, Cosima and Scott work with Dr. Nealon to understand Cosima's recovery, despite her and Scott's lack of trust for him. Alison and Donnie hatch a plan to turn the tide for her campaign by buying Ramon's drugs.

3. Formalized, Complex, and Costly

Art and Sarah work together to find a lead on Mark's location. Mark reveals to Gracie that he was sent by the military to infiltrate the Proletheans to find the original Castor DNA, which he believes Henrik entrusted to farmer Willard Finch for safe keeping. It is believed the DNA would be used to cure the Castor defect. Gracie recovers the box from Finch, but there is no DNA inside. Henrik's wife Bonnie tracks Gracie down to bring her back to the Proletheans. Sarah learns that Art is devoted to helping the Clone Club because he was in love with Beth. Cosima extracts Seth's brain and learns that like the Leda clones, the Castor clones are also suffering from a defect, albeit a neurological one, as well as determining that both sets of clones are biological siblings. Alison gains support for her campaign after selling the other mothers drugs hidden in bars of soap. Nealon treats Rachel's brain damage. Rudy confronts Finch but he dies from a heart attack during the torture. Sarah's arrival is soon followed by Bonnie, who shoots Mark.

4. Newer Elements of Our Defense

Sarah evades Bonnie and escapes with a wounded Mark. They arrive at an empty house where Sarah treats Mark's wounds. When Mark loses consciousness, Sarah recovers his motel key and finds Henrik's box, where she learns he worked with Ethan, and Henrik used the DNA to produce his own clone, Abel. When Mark finds her, he reveals the baby died shortly after birth, so they go to a grave yard to recover his body. Gracie's pregnancy ends with a miscarriage, and Bonnie, believing it to be punishment from God for marrying Mark, shuns her. Alison finds herself wanted by Ramon's boss, who is revealed to be her ex-boyfriend Jason Kellerman. The two decide to work together to distribute the drugs. Felix sets up a dating profile for Cosima to get over Delphine. Helena manages to escape from her cell and comes across a sick Castor clone, Parsons, that Coady is experimenting on. Helena kills him out of mercy before she is captured again. Sarah recovers Abel's remains, but it is intercepted by Rudy. Sarah attempts to flee, but Mark and Rudy capture her.

5. Scarred by Many Past Frustrations

Sarah is taken to the Castor base, much to Paul's dismay; Mark would have let her go, but since deranged Rudy was there, this was the best option. Sarah also has a strained reunion with Helena, who blames her for her capture; Coady had been feeding her lies about the capture, indicating Sarah, not Siobhan was responsible. Although Coady assures Paul no harm would come to Sarah, she still collects a lot of her blood to gather stem cells. Cosima goes on a blind date with Shay Davydov ( Ksenia Solo ), a holistic healer, and quickly begins a physical relationship. However, the date is monitored. Gracie, with nowhere to go, approaches Art, who takes her to Felix and Mrs. S. There, Gracie comes out of her shell and parties with the others, getting drunk before suffering a seizure, displaying bloodshot eyes. Sarah and Helena plot an escape, and Helena successfully exits her cell, but she decides to leave Sarah behind. As she is about to leave the compound, she begins to have second thoughts. Art also meets with the woman assaulted by Rudy and Seth, learning that she has the same symptoms as Gracie.

6. Certain Agony of the Battlefield

Paul discovers the hair samples from the women the Castor clones assaulted, and that Sarah is suffering from negative side effects after being given some of Rudy's blood. Alison makes significant money from the drug deals and plots with Jason to expand further by buying her mother's beauty shop Bubbles to be used as a front. In an attempt to find Sarah, Felix has Scott bring him to Rachel to learn her location but Rachel does not know. However, Scott realizes that Rachel was painting symbols from Ethan's notes. Cosima examines Gracie and learns that the Castors' defect is sexually transmitted and renders women infertile. Paul has Coady arrested and takes charge of the base until reinforcements arrive. However, he later realizes that even his superior David Benchman is conspiring against him, as Coady is planning to weaponize the defect. Rudy is recalled from searching for Helena to help Coady. Paul helps Sarah, who has recovered, to escape, but he decides to stay behind. He kills a Castor clone, Miller, but is stabbed in the process. Paul urges Coady to stop. When she responds by shooting him, a dying Paul releases a grenade, destroying Abel's remains. Helena, who returned, finds Sarah on the way out.

7. Community of Dreadful Fear and Hate

After escaping the Castor camp, Sarah and Helena meet Mrs. S. at a local bar, where Helena wants to kill her for selling her out. After heated discussion, Mrs. S promises that Sarah, Kira, Felix, herself and all the other "sisters" will be the family Helena never had. Delphine asks Cosima for a urine sample, but Cosima double crosses her by asking Alison to give hers. Meanwhile, Alison's mother Connie refuses to sell her store. When Donnie and Jason try to pay their supplier Pouchie, Donnie accidentally gives Alison's signatures that support her campaign instead. Pouchie holds Donnie until the money arrives. Alison and Felix attend a campaign event at a local school where Felix arranges for Cosima to pose as Alison for the photography shoot. Alison pays Pouchie, and she has Donnie released. She then takes over from Cosima-as-Alison and gives an impassioned campaign speech, gaining more support over Marci. Connie decides to sign the papers to Bubbles. Alison turns down Cosima's attempt to substitute a urine sample, suspecting her illness has resurfaced when she begins coughing again. Later, Cosima experiences bleeding from her groin during a bath. Scott spends time with Rachel in order to decode Ethan's notes.

8. Ruthless in Purpose, and Insidious in Method

Delphine meets the Leda clone Krystal and afterward informs Nealon that Krystal has no idea about clones. David Benchman informs Coady that they have infiltrated Dyad. Rachel will only decode the symbols in Ethan's The Island of Doctor Moreau book if Sarah and Scott help her escape to Taiwan with a new life using Krystal's identity. Sarah and Felix go to Krystal's place of work, a beauty salon, where Felix poses as a customer to steal her wallet. Felix discovers that although Krystal is not a self-aware clone, she began investigating her attempted kidnapping by Rudy and Seth. Rudy shows up at Scott's apartment and steals Ethan's book by threatening Scott's cat. Delphine suspects that Rachel or Shay have been spying for Castor people. Delphine fires Scott for not reporting the book earlier; Scott previously made a copy of the book. Cosima refuses to accept more treatment using Kira's stem cells, and she resigns from Dyad. Rachel begins translating but Nealon busts in, taking her and the book before smuggling Rachel away for prosthetic eye surgery using Krystal's identity. The Neolutionists have held the real Krystal in a medically-induced coma in Rachel's place at Dyad, to fool Delphine and the other clones. From what they saw translated, Mrs. S, Felix, and Sarah believe the Castor original is in London.

9. Insolvent Phantom of Tomorrow

Felix, Sarah and Mrs. S arrive in London to meet with Terrance who believes Ethan's coded numbers relate to a prisoner identity. As Terrance investigates, Ferdinand has him beaten to death. Cosima comes to believe that Shay is a spy working for Castor. When Delphine interrogates Shay, she intends to stage her death as a suicide. However, Cosima calls her off because Gracie admits that she betrayed them to help Mark. Pouchie demands that Donnie return the drugs, keeping the canister with Helena's eggs as collateral. Donnie and Helena return the drugs, but Helena kills Pouchie and his crew after they threaten Alison's children, and takes all of the money. Mrs. S previously stated that to stop all the danger, the only way is to kill the original source; but when the dying Terrance whispers what he found out, Mrs. S insists that she, Sarah and Felix return home and stop investigating. Sarah takes Terrance's phone, leading to the address of Kendall Mallone, Siobhan's mother. Kendall reveals that she submitted to Ethan's medical tests while in prison, and she is the original to both Leda and Castor as she is a chimera carrying two genetic lines; Kendall absorbed a male twin in her mother's womb.

10. History Yet to Be Written

Kendall returns with the others to Canada, with Art's assistance. Cosima later obtains biological material from Kendall. Doctor Coady has Rudy follow Alison, who lures Rudy to her garage, where Helena waits to kill him. Delphine and Sarah make a deal with Ferdinand to stop Coady. Sarah and Felix find Gracie and Mark; Mark assists them by posing as Rudy and giving Coady a location for Kendall, where Ferdinand captures Coady. Kendall reveals that she arranged for Sarah to arrive in S's care. Delphine realizes that Krystal has taken Rachel's place in Dyad's ward, and has Nealon arrested. Nealon reveals that Neolution runs both Leda and Castor, and that Rachel is in their custody. Delphine is forced to kill Nealon when he attacks her and tries to place a worm into her mouth. Upon learning of Nealon's Neolutionist agenda, Ferdinand, who despises Neolution, defects. The Clone Club and their families, along with Art and Scott, gather at Bubbles to celebrate their victory and Alison's election win, and to remember Beth. Delphine reconciles with Cosima, before being shot by an unseen figure. Rachel, with a new prosthetic eye, is being held in a house where she reunites with Charlotte and another woman, her presumed-dead adoptive mother Susan. In Iceland, Kendall goes into hiding and Sarah reunites with Kira.